metauto.pl (gH) version 1.3

 Step 1:  build stability.files and determine factors

 required file alpha-div.mothur is present
 required file beta-div.mothur is present
 required file calc_abundance.pl is present
 required file elim_LowFreqOTU_from_shared.pl is present
 required file groups.mothur is present
 required file quality.mothur is present
 required file silva.v4.fasta is present
 required file test16S.oligos is present
 required file trainset9_032012.pds.fasta is present
 required file trainset9_032012.pds.tax is present

 2 files written in stability.files for *R1.fastq files.

 -- 2 stability.files *R1* and *R2* used.
 
 voici les 1 séries : S01
 voici les 2 facteurs : H0 H24

 -- step 1 completed.


 Step 2:  check quality of fragments

-- mothur quality.mothur 

mothur v.1.33.3
Last updated: 4/4/2014

by
Patrick D. Schloss

Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

Type 'quit()' to exit program



mothur > make.contigs(file=stability.files, processors=8, insert=20, deltaq=5, oligos=test16S.oligos)

Using 8 processors.
Reading fastq data...
10000
20000
30000
[...]
90000
100000
110000
120000
129475
Done.

>>>>>   Processing S01-H0_ATCACG_L001_R1.0ffastatemp (file 1 of 2)   <<<<<
Making contigs...
1000
Done.

>>>>>   Processing S01-H0_ATCACG_L001_R1.0ffastatemp (file 1 of 2)   <<<<<
Making contigs...
1000
Done.

>>>>>   Processing S01-H0_ATCACG_L001_R1.0ffastatemp (file 1 of 2)   <<<<<
Making contigs...
1000
Done.

>>>>>   Processing S01-H0_ATCACG_L001_R1.0ffastatemp (file 1 of 2)   <<<<<
Making contigs...
1000
Done.

>>>>>   Processing S01-H0_ATCACG_L001_R1.0ffastatemp (file 1 of 2)   <<<<<
Making contigs...
1000
Done.

>>>>>   Processing S01-H0_ATCACG_L001_R1.0ffastatemp (file 1 of 2)   <<<<<
Making contigs...
1000
Done.

>>>>>   Processing S01-H0_ATCACG_L001_R1.0ffastatemp (file 1 of 2)   <<<<<
Making contigs...
1000
Done.

>>>>>   Processing S01-H0_ATCACG_L001_R1.0ffastatemp (file 1 of 2)   <<<<<
Making contigs...
1000
2000
[...]
15273
15273
15273
15273
Done.

>>>>>   Processing S01-H24_GTAAGT_L001_R1.0ffastatemp (file 2 of 2)   <<<<<
Making contigs...
1000
Done.

>>>>>   Processing S01-H24_GTAAGT_L001_R1.0ffastatemp (file 2 of 2)   <<<<<
Making contigs...
1000
Done.

>>>>>   Processing S01-H24_GTAAGT_L001_R1.0ffastatemp (file 2 of 2)   <<<<<
Making contigs...
1000
Done.

>>>>>   Processing S01-H24_GTAAGT_L001_R1.0ffastatemp (file 2 of 2)   <<<<<
Making contigs...
1000
Done.

>>>>>   Processing S01-H24_GTAAGT_L001_R1.0ffastatemp (file 2 of 2)   <<<<<
Making contigs...
1000
Done.

>>>>>   Processing S01-H24_GTAAGT_L001_R1.0ffastatemp (file 2 of 2)   <<<<<
Making contigs...
1000
Done.

>>>>>   Processing S01-H24_GTAAGT_L001_R1.0ffastatemp (file 2 of 2)   <<<<<
Making contigs...
1000
Done.

>>>>>   Processing S01-H24_GTAAGT_L001_R1.0ffastatemp (file 2 of 2)   <<<<<
Making contigs...
1000
2000
2000
[...]
16185
16000
16185
Done.
It took 68 secs to process 251659 sequences.

Group count: 
S01-H0_ATCACG_L001_   67380
S01-H24_GTAAGT_L001_   85060
Total of all groups is 152440

Output File Names: 
stability.trim.contigs.fasta
stability.contigs.report
stability.scrap.contigs.fasta
stability.contigs.groups

[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.

mothur > system(mv stability.trim.contigs.fasta stability.trim.contigs.16S.fasta)


mothur > system(mv stability.contigs.groups stability.contigs.16S.groups)


mothur > summary.seqs(fasta=stability.trim.contigs.16S.fasta, processors=8)

Using 8 processors.

Using 8 processors.
[...]

      Start   End   NBases   Ambigs   Polymer   NumSeqs
Minimum:   1   227   227   0   3   1
2.5%-tile:   1   251   251   0   4   3812
25%-tile:   1   253   253   0   5   38111
Median:    1   253   253   0   5   76221
75%-tile:   1   253   253   0   6   114331
97.5%-tile:   1   446   446   6   14   148630
Maximum:   1   460   460   90   207   152440
Mean:   1   262.189   262.189   0.510988   5.59096
# of Seqs:   152440

Output File Names: 
stability.trim.contigs.16S.summary

mothur > screen.seqs(fasta=stability.trim.contigs.16S.fasta, group=stability.contigs.16S.groups, summary=stability.trim.contigs.16S.summary, maxambig=0, maxlength=253, processors=8, maxhomop=7)

Using 8 processors.
Processing sequence: 100
Processing sequence: 200
[...]
Processing sequence: 15400
Processing sequence: 1550

Using 8 processors.
Processing sequence: 100
Processing sequence: 200
[...]
Processing sequence: 19341

Output File Names: 
stability.trim.contigs.16S.good.summary
stability.trim.contigs.16S.good.fasta
stability.trim.contigs.16S.bad.accnos
stability.contigs.16S.good.groups


It took 1 secs to screen 152440 sequences.

mothur > summary.seqs(fasta=stability.trim.contigs.16S.good.fasta)

Using 8 processors.

[...]

      Start   End   NBases   Ambigs   Polymer   NumSeqs
Minimum:   1   227   227   0   3   1
2.5%-tile:   1   252   252   0   4   3171
25%-tile:   1   253   253   0   4   31707
Median:    1   253   253   0   5   63414
75%-tile:   1   253   253   0   5   95120
97.5%-tile:   1   253   253   0   6   123656
Maximum:   1   253   253   0   7   126826
Mean:   1   252.951   252.951   0   4.97361
# of Seqs:   126826

Output File Names: 
stability.trim.contigs.16S.good.summary


mothur > unique.seqs(fasta=stability.trim.contigs.16S.good.fasta)
1000   499
2000   920
[...]
126826   18081

Output File Names: 
stability.trim.contigs.16S.good.names
stability.trim.contigs.16S.good.unique.fasta


mothur > count.seqs(name=stability.trim.contigs.16S.good.names, group=stability.contigs.16S.good.groups)

Using 8 processors.

[...]
It took 0 secs to create a table for 126826 sequences.


Total number of sequences: 126826

Output File Names: 
stability.trim.contigs.16S.good.count_table


mothur > summary.seqs(fasta=stability.trim.contigs.16S.good.unique.fasta, count=stability.trim.contigs.16S.good.count_table)

Using 8 processors.

[...]
      Start   End   NBases   Ambigs   Polymer   NumSeqs
Minimum:   1   227   227   0   3   1
2.5%-tile:   1   252   252   0   4   3171
25%-tile:   1   253   253   0   4   31707
Median:    1   253   253   0   5   63414
75%-tile:   1   253   253   0   5   95120
97.5%-tile:   1   253   253   0   6   123656
Maximum:   1   253   253   0   7   126826
Mean:   1   252.951   252.951   0   4.97361
# of unique seqs:   18081
total # of seqs:   126826

Output File Names: 
stability.trim.contigs.16S.good.unique.summary


mothur > align.seqs(fasta=stability.trim.contigs.16S.good.unique.fasta, reference=silva.v4.fasta)

Using 8 processors.

Reading in the silva.v4.fasta template sequences...   DONE.
It took 3 to read  14956 sequences.
Aligning sequences from stability.trim.contigs.16S.good.unique.fasta ...
100
200
300
[...]
2200
2261
Some of you sequences generated alignments that eliminated too many bases, a list is provided in stability.trim.contigs.16S.good.unique.flip.accnos. If you set the flip parameter to true mothur will try aligning the reverse compliment as well.
It took 7 secs to align 18081 sequences.


Output File Names: 
stability.trim.contigs.16S.good.unique.align
stability.trim.contigs.16S.good.unique.align.report
stability.trim.contigs.16S.good.unique.flip.accnos


mothur > summary.seqs(fasta=stability.trim.contigs.16S.good.unique.align, count=stability.trim.contigs.16S.good.count_table)

Using 8 processors.

[...]
      Start   End   NBases   Ambigs   Polymer   NumSeqs
Minimum:   1   1   1   0   1   1
2.5%-tile:   1968   11550   252   0   4   3171
25%-tile:   1968   11550   253   0   4   31707
Median:    1968   11550   253   0   5   63414
75%-tile:   1968   11550   253   0   5   95120
97.5%-tile:   1968   11550   253   0   6   123656
Maximum:   13404   13425   253   0   7   126826
Mean:   1976.42   11551.3   252.786   0   4.97191
# of unique seqs:   18081
total # of seqs:   126826

Output File Names: 
stability.trim.contigs.16S.good.unique.summary


mothur > screen.seqs(fasta=stability.trim.contigs.16S.good.unique.align, count=stability.trim.contigs.16S.good.count_table, start=1968, end=11550)

Using 8 processors.
Processing sequence: 100
Processing sequence: 200
[...]
Processing sequence: 2200
Processing sequence: 2261

Output File Names: 
stability.trim.contigs.16S.good.unique.good.align
stability.trim.contigs.16S.good.unique.bad.accnos
stability.trim.contigs.16S.good.good.count_table


It took 1 secs to screen 18081 sequences.

mothur > summary.seqs(fasta=stability.trim.contigs.16S.good.unique.good.align, count=stability.trim.contigs.16S.good.good.count_table)

Using 8 processors.
[...]

      Start   End   NBases   Ambigs   Polymer   NumSeqs
Minimum:   1965   11550   227   0   3   1
2.5%-tile:   1968   11550   253   0   4   3164
25%-tile:   1968   11550   253   0   4   31639
Median:    1968   11550   253   0   5   63278
75%-tile:   1968   11550   253   0   5   94917
97.5%-tile:   1968   11550   253   0   6   123392
Maximum:   1968   11550   253   0   7   126555
Mean:   1968   11550   252.973   0   4.97288
# of unique seqs:   17969
total # of seqs:   126555

Output File Names: 
stability.trim.contigs.16S.good.unique.good.summary


mothur > filter.seqs(fasta=stability.trim.contigs.16S.good.unique.good.align, vertical=T, trump=.)

Using 8 processors.
Creating Filter... 
100
100
[...]
2246
2247


Running Filter... 
100
200
300
[...]
2247



Length of filtered alignment: 363
Number of columns removed: 13062
Length of the original alignment: 13425
Number of sequences used to construct filter: 17969

Output File Names: 
stability.filter
stability.trim.contigs.16S.good.unique.good.filter.fasta


mothur > unique.seqs(fasta=stability.trim.contigs.16S.good.unique.good.filter.fasta, count=stability.trim.contigs.16S.good.good.count_table)
1000   1000
2000   2000
[...]
16000   16000
17000   17000
17969   17969

Output File Names: 
stability.trim.contigs.16S.good.unique.good.filter.count_table
stability.trim.contigs.16S.good.unique.good.filter.unique.fasta


mothur > pre.cluster(fasta=stability.trim.contigs.16S.good.unique.good.filter.unique.fasta, count=stability.trim.contigs.16S.good.unique.good.filter.count_table, diffs=2)

Using 8 processors.

Processing group S01-H0_ATCACG_L001_:

Using 8 processors.

Processing group S01-H24_GTAAGT_L001_:
0   5451   1199
100   2480   4170
200   2314   4336
[...]
6500   1376   5274
6600   1376   5274
6650   1376   5274
Total number of sequences before pre.cluster was 6650.
pre.cluster removed 5274 sequences.

It took 1 secs to cluster 6650 sequences.
0   11151   1091
100   7902   4340
200   7569   4673
300   7382   4860
[...]
12200   5011   7231
12242   5011   7231
Total number of sequences before pre.cluster was 12242.
pre.cluster removed 7231 sequences.

It took 4 secs to cluster 12242 sequences.
It took 4 secs to run pre.cluster.

Output File Names: 
stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.fasta
stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.count_table
stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.S01-H0_ATCACG_L001_.map
stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.S01-H24_GTAAGT_L001_.map


mothur > summary.seqs(fasta=stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.fasta, count=stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.count_table)

Using 8 processors.
[...]

      Start   End   NBases   Ambigs   Polymer   NumSeqs
Minimum:   1   363   227   0   3   1
2.5%-tile:   1   363   253   0   4   3164
25%-tile:   1   363   253   0   4   31639
Median:    1   363   253   0   5   63278
75%-tile:   1   363   253   0   5   94917
97.5%-tile:   1   363   253   0   6   123392
Maximum:   1   363   253   0   7   126555
Mean:   1   363   252.977   0   4.97243
# of unique seqs:   6265
total # of seqs:   126555

Output File Names: 
stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.summary


mothur > chimera.uchime(fasta=stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.fasta, count=stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.count_table, dereplicate=t)

Using 8 processors.

uchime by Robert C. Edgar
http://drive5.com/uchime
This code is donated to the public domain.

Checking sequences from stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.fasta ...
uchime v4.2.40
by Robert C. Edgar
http://drive5.com/uchime
This code is donated to the public domain.

uchime v4.2.40
by Robert C. Edgar
http://drive5.com/uchime
This code is donated to the public domain.


It took 11 secs to check 1376 sequences from group S01-H24_GTAAGT_L001_.

It took 80 secs to check 5011 sequences from group S01-H0_ATCACG_L001_.

Output File Names: 
stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.uchime.pick.count_table
stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.uchime.chimeras
stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.uchime.accnos


mothur > remove.seqs(fasta=stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.fasta, accnos=stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.uchime.accnos)
[WARNING]: This command can take a namefile and you did not provide one. The current namefile is stability.trim.contigs.16S.good.names which seems to match stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.fasta.
Removed 2409 sequences from your fasta file.

Output File Names: 
stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.pick.fasta


mothur > summary.seqs(fasta=stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.pick.fasta, count=stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.uchime.pick.count_table)

Using 8 processors.

[...]

      Start   End   NBases   Ambigs   Polymer   NumSeqs
Minimum:   1   363   227   0   3   1
2.5%-tile:   1   363   253   0   4   3029
25%-tile:   1   363   253   0   4   30281
Median:    1   363   253   0   5   60562
75%-tile:   1   363   253   0   5   90842
97.5%-tile:   1   363   253   0   6   118094
Maximum:   1   363   253   0   7   121122
Mean:   1   363   252.979   0   4.98348
# of unique seqs:   3856
total # of seqs:   121122

Output File Names: 
stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.pick.summary


mothur > classify.seqs(fasta=stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.pick.fasta, count=stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.uchime.pick.count_table, reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax, cutoff=60, processors=8)

Using 8 processors.
Reading template taxonomy...     DONE.
Reading template probabilities...     DONE.
It took 4 seconds get probabilities. 
Classifying sequences from stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.pick.fasta ...
Processing sequence: 100
Processing sequence: 200
[...]
Processing sequence: 482

It took 10 secs to classify 3856 sequences.


It took 0 secs to create the summary file for 3856 sequences.


Output File Names: 
stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.pick.pds.wang.taxonomy
stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.pick.pds.wang.tax.summary


mothur > remove.lineage(fasta=stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.pick.fasta, count=stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.uchime.pick.count_table, taxonomy=stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.pick.pds.wang.taxonomy, taxon=Chloroplast-Mitochondria-unknown-Archaea-Eukaryota)

[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.


Output File Names: 
stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy
stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.pick.pick.fasta
stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.uchime.pick.pick.count_table


mothur > summary.seqs(fasta=stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.pick.pick.fasta, count=stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.uchime.pick.pick.count_table)

Using 8 processors.

[...]

      Start   End   NBases   Ambigs   Polymer   NumSeqs
Minimum:   1   363   227   0   3   1
2.5%-tile:   1   363   252   0   4   1870
25%-tile:   1   363   253   0   4   18696
Median:    1   363   253   0   5   37391
75%-tile:   1   363   253   0   6   56086
97.5%-tile:   1   363   253   0   6   72912
Maximum:   1   363   253   0   7   74781
Mean:   1   363   252.97   0   4.97313
# of unique seqs:   3349
total # of seqs:   74781

Output File Names: 
stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.pick.pick.summary


mothur > system(mv stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.uchime.pick.pick.count_table 16S.count_table)


mothur > system(mv stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.pick.pick.fasta  16S.fasta)


mothur > system(mv stability.trim.contigs.16S.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy 16S.taxonomy)


mothur > system(echo ok > mothur1.ok )

mothur > quit()

 -- step 2 completed.


 Step 3:  build groups (long)

-- mothur groups.mothur 

mothur v.1.33.3
Last updated: 4/4/2014

by
Patrick D. Schloss

Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

Type 'quit()' to exit program

mothur > cluster.split(fasta=16S.fasta, count=16S.count_table, taxonomy=16S.taxonomy, splitmethod=classify, taxlevel=4, cutoff=0.15, method=average, processors=1)

Using 1 processors.
Using splitmethod fasta.
Splitting the file...
/******************************************/

Using 1 processors.
/******************************************/
0   0
100   0
200   0
201   0

Output File Names: 
16S.fasta.0.dist

It took 0 to calculate the distances for 202 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
50   0

Output File Names: 
16S.fasta.1.dist

It took 0 to calculate the distances for 51 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
100   0
200   0
300   0
400   1
482   1

Output File Names: 
16S.fasta.2.dist

It took 1 to calculate the distances for 483 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
54   0

Output File Names: 
16S.fasta.3.dist

It took 0 to calculate the distances for 55 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
100   0
200   0
270   0

Output File Names: 
16S.fasta.4.dist

It took 0 to calculate the distances for 271 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
100   0
200   0
300   0
400   0
500   1
600   1
638   1

Output File Names: 
16S.fasta.5.dist

It took 1 to calculate the distances for 639 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
99   0

Output File Names: 
16S.fasta.6.dist

It took 0 to calculate the distances for 100 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
5   0

Output File Names: 
16S.fasta.7.dist

It took 0 to calculate the distances for 6 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
100   0
174   0

Output File Names: 
16S.fasta.8.dist

It took 0 to calculate the distances for 175 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
3   0

Output File Names: 
16S.fasta.9.dist

It took 0 to calculate the distances for 4 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
82   0

Output File Names: 
16S.fasta.10.dist

It took 0 to calculate the distances for 83 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
21   0

Output File Names: 
16S.fasta.11.dist

It took 0 to calculate the distances for 22 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
100   0
148   0

Output File Names: 
16S.fasta.12.dist

It took 0 to calculate the distances for 149 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
100   0
167   0

Output File Names: 
16S.fasta.13.dist

It took 0 to calculate the distances for 168 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
14   0

Output File Names: 
16S.fasta.14.dist

It took 0 to calculate the distances for 15 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
100   0
149   0

Output File Names: 
16S.fasta.15.dist

It took 0 to calculate the distances for 150 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
41   0

Output File Names: 
16S.fasta.16.dist

It took 0 to calculate the distances for 42 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
5   0

Output File Names: 
16S.fasta.17.dist

It took 0 to calculate the distances for 6 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
26   0

Output File Names: 
16S.fasta.18.dist

It took 0 to calculate the distances for 27 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
44   0

Output File Names: 
16S.fasta.19.dist

It took 0 to calculate the distances for 45 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
11   0

Output File Names: 
16S.fasta.20.dist

It took 0 to calculate the distances for 12 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
21   0

Output File Names: 
16S.fasta.21.dist

It took 0 to calculate the distances for 22 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
49   0

Output File Names: 
16S.fasta.22.dist

It took 0 to calculate the distances for 50 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
18   0

Output File Names: 
16S.fasta.23.dist

It took 0 to calculate the distances for 19 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
77   0

Output File Names: 
16S.fasta.24.dist

It took 0 to calculate the distances for 78 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
21   0

Output File Names: 
16S.fasta.25.dist

It took 0 to calculate the distances for 22 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
36   0

Output File Names: 
16S.fasta.26.dist

It took 0 to calculate the distances for 37 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
8   0

Output File Names: 
16S.fasta.27.dist

It took 0 to calculate the distances for 9 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
16   0

Output File Names: 
16S.fasta.28.dist

It took 0 to calculate the distances for 17 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
29   0

Output File Names: 
16S.fasta.29.dist

It took 0 to calculate the distances for 30 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
36   0

Output File Names: 
16S.fasta.30.dist

It took 0 to calculate the distances for 37 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
42   0

Output File Names: 
16S.fasta.31.dist

It took 0 to calculate the distances for 43 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
10   0

Output File Names: 
16S.fasta.32.dist

It took 0 to calculate the distances for 11 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
59   0

Output File Names: 
16S.fasta.33.dist

It took 0 to calculate the distances for 60 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
3   0

Output File Names: 
16S.fasta.34.dist

It took 0 to calculate the distances for 4 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
22   0

Output File Names: 
16S.fasta.35.dist

It took 0 to calculate the distances for 23 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
6   0

Output File Names: 
16S.fasta.36.dist

It took 0 to calculate the distances for 7 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
20   0

Output File Names: 
16S.fasta.37.dist

It took 0 to calculate the distances for 21 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
1   0
16S.fasta.38.dist is blank. This can result if there are no distances below your cutoff.

Output File Names: 
16S.fasta.38.dist

It took 0 to calculate the distances for 2 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
15   0

Output File Names: 
16S.fasta.39.dist

It took 0 to calculate the distances for 16 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
1   0

Output File Names: 
16S.fasta.40.dist

It took 0 to calculate the distances for 2 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
6   0

Output File Names: 
16S.fasta.41.dist

It took 0 to calculate the distances for 7 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
3   0

Output File Names: 
16S.fasta.42.dist

It took 0 to calculate the distances for 4 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
2   0

Output File Names: 
16S.fasta.43.dist

It took 0 to calculate the distances for 3 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
22   0

Output File Names: 
16S.fasta.44.dist

It took 0 to calculate the distances for 23 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
4   0

Output File Names: 
16S.fasta.45.dist

It took 0 to calculate the distances for 5 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
7   0

Output File Names: 
16S.fasta.46.dist

It took 0 to calculate the distances for 8 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
4   0

Output File Names: 
16S.fasta.47.dist

It took 0 to calculate the distances for 5 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
2   0

Output File Names: 
16S.fasta.48.dist

It took 0 to calculate the distances for 3 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
3   0

Output File Names: 
16S.fasta.49.dist

It took 0 to calculate the distances for 4 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
2   0

Output File Names: 
16S.fasta.50.dist

It took 0 to calculate the distances for 3 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
4   0

Output File Names: 
16S.fasta.51.dist

It took 0 to calculate the distances for 5 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
4   0

Output File Names: 
16S.fasta.52.dist

It took 0 to calculate the distances for 5 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
2   0

Output File Names: 
16S.fasta.53.dist

It took 0 to calculate the distances for 3 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
1   0
16S.fasta.54.dist is blank. This can result if there are no distances below your cutoff.

Output File Names: 
16S.fasta.54.dist

It took 0 to calculate the distances for 2 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
2   0

Output File Names: 
16S.fasta.55.dist

It took 0 to calculate the distances for 3 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
2   0

Output File Names: 
16S.fasta.56.dist

It took 0 to calculate the distances for 3 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
13   0

Output File Names: 
16S.fasta.57.dist

It took 0 to calculate the distances for 14 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
2   0

Output File Names: 
16S.fasta.58.dist

It took 0 to calculate the distances for 3 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
2   0

Output File Names: 
16S.fasta.59.dist

It took 0 to calculate the distances for 3 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
3   0

Output File Names: 
16S.fasta.60.dist

It took 0 to calculate the distances for 4 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
1   0

Output File Names: 
16S.fasta.61.dist

It took 0 to calculate the distances for 2 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
1   0

Output File Names: 
16S.fasta.62.dist

It took 0 to calculate the distances for 2 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
1   0

Output File Names: 
16S.fasta.63.dist

It took 0 to calculate the distances for 2 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
1   0

Output File Names: 
16S.fasta.64.dist

It took 0 to calculate the distances for 2 sequences.
/******************************************/

Using 1 processors.
/******************************************/
0   0
1   0

Output File Names: 
16S.fasta.65.dist

It took 0 to calculate the distances for 2 sequences.
It took 2 seconds to split the distance file.

Reading 16S.fasta.5.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.5.dist
Cutoff was 0.155 changed cutoff to 0.07

Reading 16S.fasta.2.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.2.dist
Cutoff was 0.155 changed cutoff to 0.08

Reading 16S.fasta.4.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.4.dist
Cutoff was 0.155 changed cutoff to 0.11

Reading 16S.fasta.8.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.8.dist
Cutoff was 0.155 changed cutoff to 0.11

Reading 16S.fasta.13.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.13.dist
Cutoff was 0.155 changed cutoff to 0.08

Reading 16S.fasta.12.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.12.dist
Cutoff was 0.155 changed cutoff to 0.09

Reading 16S.fasta.6.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.6.dist

Reading 16S.fasta.10.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.10.dist
Cutoff was 0.155 changed cutoff to 0.08

Reading 16S.fasta.15.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.15.dist
Cutoff was 0.155 changed cutoff to 0.1

Reading 16S.fasta.24.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.24.dist
Cutoff was 0.155 changed cutoff to 0.1

Reading 16S.fasta.3.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.3.dist
Cutoff was 0.155 changed cutoff to 0.1

Reading 16S.fasta.1.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.1.dist
Cutoff was 0.155 changed cutoff to 0.12

Reading 16S.fasta.33.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.33.dist
Cutoff was 0.155 changed cutoff to 0.1

Reading 16S.fasta.0.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.0.dist
Cutoff was 0.155 changed cutoff to 0.1

Reading 16S.fasta.22.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.22.dist
Cutoff was 0.155 changed cutoff to 0.11

Reading 16S.fasta.19.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.19.dist
Cutoff was 0.155 changed cutoff to 0.14

Reading 16S.fasta.16.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.16.dist
Cutoff was 0.155 changed cutoff to 0.09

Reading 16S.fasta.26.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.26.dist
Cutoff was 0.155 changed cutoff to 0.09

Reading 16S.fasta.31.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.31.dist
Cutoff was 0.155 changed cutoff to 0.12

Reading 16S.fasta.35.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.35.dist

Reading 16S.fasta.25.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.25.dist

Reading 16S.fasta.18.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.18.dist
Cutoff was 0.155 changed cutoff to 0.12

Reading 16S.fasta.11.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.11.dist

Reading 16S.fasta.21.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.21.dist

Reading 16S.fasta.23.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.23.dist
Cutoff was 0.155 changed cutoff to 0.11

Reading 16S.fasta.37.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.37.dist
Cutoff was 0.155 changed cutoff to 0.1

Reading 16S.fasta.44.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.44.dist
Cutoff was 0.155 changed cutoff to 0.13

Reading 16S.fasta.39.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.39.dist

Reading 16S.fasta.29.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.29.dist
Cutoff was 0.155 changed cutoff to 0.12

Reading 16S.fasta.14.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.14.dist

Reading 16S.fasta.57.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.57.dist

Reading 16S.fasta.30.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.30.dist
Cutoff was 0.155 changed cutoff to 0.14

Reading 16S.fasta.20.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.20.dist
Cutoff was 0.155 changed cutoff to 0.12

Reading 16S.fasta.32.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.32.dist

Reading 16S.fasta.28.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.28.dist
Cutoff was 0.155 changed cutoff to 0.13

Reading 16S.fasta.36.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.36.dist

Reading 16S.fasta.7.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.7.dist

Reading 16S.fasta.27.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.27.dist

Reading 16S.fasta.45.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.45.dist

Reading 16S.fasta.51.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.51.dist

Reading 16S.fasta.52.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.52.dist

Reading 16S.fasta.41.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.41.dist

Reading 16S.fasta.17.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.17.dist
Cutoff was 0.155 changed cutoff to 0.14

Reading 16S.fasta.9.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.9.dist

Reading 16S.fasta.60.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.60.dist

Reading 16S.fasta.42.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.42.dist
Cutoff was 0.155 changed cutoff to 0.16

Reading 16S.fasta.48.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.48.dist

Reading 16S.fasta.34.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.34.dist

Reading 16S.fasta.46.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.46.dist

Reading 16S.fasta.50.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.50.dist

Reading 16S.fasta.59.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.59.dist

Reading 16S.fasta.53.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.53.dist

Reading 16S.fasta.56.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.56.dist
Cutoff was 0.155 changed cutoff to 0.16

Reading 16S.fasta.49.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.49.dist

Reading 16S.fasta.47.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.47.dist

Reading 16S.fasta.40.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.40.dist

Reading 16S.fasta.62.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.62.dist

Reading 16S.fasta.55.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.55.dist

Reading 16S.fasta.58.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.58.dist

Reading 16S.fasta.63.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.63.dist

Reading 16S.fasta.64.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.64.dist

Reading 16S.fasta.43.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.43.dist

Reading 16S.fasta.61.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.61.dist

Reading 16S.fasta.65.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************

Clustering 16S.fasta.65.dist
Cutoff was 0.155 changed cutoff to 0.07
It took 1 seconds to cluster
Merging the clustered files...
It took 0 seconds to merge.

Output File Names: 
16S.an.unique_list.list


mothur > make.shared(list=16S.an.unique_list.list, count=16S.count_table, label=0.03)
0.03

Output File Names: 
16S.an.unique_list.shared
16S.an.unique_list.S01-H0_ATCACG_L001_.rabund
16S.an.unique_list.S01-H24_GTAAGT_L001_.rabund


mothur > classify.otu(list=16S.an.unique_list.list, count=16S.count_table, taxonomy=16S.taxonomy, label=0.03)
reftaxonomy is not required, but if given will keep the rankIDs in the summary file static.
0.03   1420

Output File Names: 
16S.an.unique_list.0.03.cons.taxonomy
16S.an.unique_list.0.03.cons.tax.summary


mothur > get.oturep(method=abundance, list=16S.an.unique_list.list, label=0.03, count=16S.count_table, fasta=16S.fasta)
0.03   1420

Output File Names: 
16S.an.unique_list.0.03.rep.count_table
16S.an.unique_list.0.03.rep.fasta


mothur > create.database(list=16S.an.unique_list.list, label=0.03, repfasta=16S.an.unique_list.0.03.rep.fasta, count=16S.an.unique_list.0.03.rep.count_table, constaxonomy=16S.an.unique_list.0.03.cons.taxonomy)

Output File Names: 
16S.an.unique_list.database


mothur > system(echo ok > mothur2.ok )

mothur > quit()

 -- step 3 completed.


 Step 4:  abundance computations

-- elim_LowFreqOTU 

perl elim_LowFreqOTU_from_shared.pl -s 16S.an.unique_list.shared -f 0.1 -o 16S.an.unique_list.abund.shared

-- calc_abundance  

perl calc_abundance.pl -s 16S.an.unique_list.abund.shared -f 1000 -o 16S.an.unique_list.abund.proportion.shared

 -- step 4 completed.


 Step 5:  alpha-diversity step with R beanplots and taxonomic clustering

mothur v.1.33.3
Last updated: 4/4/2014

by
Patrick D. Schloss

Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

Type 'quit()' to exit program


mothur > summary.single(shared=16S.an.unique_list.abund.shared, calc=nseqs-coverage-sobs-chao-invsimpson-npshannon)

Processing group S01-H0_ATCACG_L001_

0.03

Processing group S01-H24_GTAAGT_L001_

0.03

Output File Names: 
16S.an.unique_list.abund.groups.summary


mothur > count.groups(shared=16S.an.unique_list.abund.shared)
S01-H0_ATCACG_L001_ contains 28378.
S01-H24_GTAAGT_L001_ contains 39802.

Total seqs: 68180.

Output File Names: 
count.summary


mothur > summary.single(shared=16S.an.unique_list.abund.shared, calc=nseqs-coverage-sobs-chao-invsimpson-npshannon, subsample=x)

Processing group S01-H0_ATCACG_L001_

0.03

Processing group S01-H24_GTAAGT_L001_

0.03

Output File Names: 
16S.an.unique_list.abund.groups.summary


mothur > summary.single(shared=16S.an.unique_list.abund.proportion.shared, calc=nseqs-coverage-sobs-chao-invsimpson-npshannon)

Processing group S01-H0_ATCACG_L001_

0.03

Processing group S01-H24_GTAAGT_L001_

0.03

Output File Names: 
16S.an.unique_list.abund.proportion.groups.summary


mothur > system(echo ok > mothur3.ok )

mothur > quit()

 -- step 5 completed.


 Step 6:  beta-diversity step

mothur v.1.33.3
Last updated: 4/4/2014

by
Patrick D. Schloss

Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

Type 'quit()' to exit program



mothur > dist.seqs(fasta=16S.an.unique_list.0.03.rep.fasta, output=phylip, processors=8)

Using 8 processors.
1100   1
1121   1

Using 8 processors.
800   1
868   1

Using 8 processors.
900   0
1000   1
1003   1

Using 8 processors.
600   1
700   1
709   1

Using 8 processors.
1200   1
1228   1

Using 8 processors.
1300   1
1327   1

Using 8 processors.
1400   1
1419   1

Using 8 processors.
0   0
100   0
200   0
300   1
400   1
500   1
501   1

Output File Names: 
16S.an.unique_list.0.03.rep.phylip.dist

It took 1 to calculate the distances for 1420 sequences.

mothur > clearcut(phylip=16S.an.unique_list.0.03.rep.phylip.dist)

Output File Names: 
16S.an.unique_list.0.03.rep.phylip.tre


mothur > unifrac.unweighted(tree=16S.an.unique_list.0.03.rep.phylip.tre, count=16S.an.unique_list.0.03.rep.count_table, distance=lt, processors=8, random=F, subsample=x)

Using 8 processors.
Tree#   Groups   UWScore   
1   S01-H0_ATCACG_L001_-S01-H24_GTAAGT_L001_   0.85511
It took 0 secs to run unifrac.unweighted.

Output File Names: 
16S.an.unique_list.0.03.rep.phylip.uwsummary
16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.dist


mothur > unifrac.weighted(tree=16S.an.unique_list.0.03.rep.phylip.tre, count=16S.an.unique_list.0.03.rep.count_table, distance=lt, processors=8, random=F, subsample=x)

Using 8 processors.
Tree#   Groups   WScore   
1   S01-H0_ATCACG_L001_-S01-H24_GTAAGT_L001_   0.694163
It took 0 secs to run unifrac.weighted.

Output File Names: 
16S.an.unique_list.0.03.rep.phylip.trewsummary
16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.dist


mothur > pcoa(phylip=16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.dist)

Processing...
Rsq 1 axis: 0
Rsq 2 axis: 0
Rsq 3 axis: 0

Output File Names: 
16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.pcoa.axes
16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.pcoa.loadings


mothur > pcoa(phylip=16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.dist)

Processing...
Rsq 1 axis: 0
Rsq 2 axis: 0
Rsq 3 axis: 0

Output File Names: 
16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.pcoa.axes
16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.pcoa.loadings


mothur > nmds(phylip=16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.dist)
Processing Dimension: 2
1
2
3
4
5
6
7
8
9
10

Number of dimensions:   2
Lowest stress :   0
R-squared for configuration:   0

Output File Names: 
16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.nmds.iters
16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.nmds.stress
16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.nmds.axes


mothur > nmds(phylip=16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.dist, mindim=3, maxdim=3)
Processing Dimension: 3
1
2
3
4
5
6
7
8
9
10

Number of dimensions:   3
Lowest stress :   0
R-squared for configuration:   0

Output File Names: 
16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.nmds.iters
16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.nmds.stress
16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.nmds.axes


mothur > nmds(phylip=16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.dist)
Processing Dimension: 2
1
2
3
4
5
6
7
8
9
10

Number of dimensions:   2
Lowest stress :   0
R-squared for configuration:   0

Output File Names: 
16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.nmds.iters
16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.nmds.stress
16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.nmds.axes


mothur > nmds(phylip=16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.dist, mindim=3, maxdim=3)
Processing Dimension: 3
1
2
3
4
5
6
7
8
9
10

Number of dimensions:   3
Lowest stress :   0
R-squared for configuration:   0

Output File Names: 
16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.nmds.iters
16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.nmds.stress
16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.nmds.axes


mothur > amova(phylip=16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.dist, design=16S.design)
[ERROR]: S01-H0_ATCACG_L001_ is not in your design file, please correct.
[ERROR]: S01-H24_GTAAGT_L001_ is not in your design file, please correct.

mothur > amova(phylip=16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.dist, design=16S.design)
[ERROR]: S01-H0_ATCACG_L001_ is not in your design file, please correct.
[ERROR]: S01-H24_GTAAGT_L001_ is not in your design file, please correct.

mothur > unifrac.unweighted(tree=16S.an.unique_list.0.03.rep.phylip.tre, count=16S.an.unique_list.abund.proportion.count_table, distance=lt, processors=8, random=F)
Unable to open 16S.an.unique_list.abund.proportion.count_table

Using 8 processors.
[ERROR]: did not complete unifrac.unweighted.

mothur > unifrac.weighted(tree=16S.an.unique_list.0.03.rep.phylip.tre, count=16S.an.unique_list.abund.proportion.count_table, distance=lt, processors=8, random=F)
Unable to open 16S.an.unique_list.abund.proportion.count_table

Using 8 processors.
[ERROR]: did not complete unifrac.weighted.

mothur > pcoa(phylip=16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.dist)

Processing...
Rsq 1 axis: 0
Rsq 2 axis: 0
Rsq 3 axis: 0

Output File Names: 
16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.pcoa.axes
16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.pcoa.loadings


mothur > pcoa(phylip=16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.dist)

Processing...
Rsq 1 axis: 0
Rsq 2 axis: 0
Rsq 3 axis: 0

Output File Names: 
16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.pcoa.axes
16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.pcoa.loadings


mothur > nmds(phylip=16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.dist)
Processing Dimension: 2
1
2
3
4
5
6
7
8
9
10

Number of dimensions:   2
Lowest stress :   0
R-squared for configuration:   0

Output File Names: 
16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.nmds.iters
16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.nmds.stress
16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.nmds.axes


mothur > nmds(phylip=16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.dist, mindim=3, maxdim=3)
Processing Dimension: 3
1
2
3
4
5
6
7
8
9
10

Number of dimensions:   3
Lowest stress :   0
R-squared for configuration:   0

Output File Names: 
16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.nmds.iters
16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.nmds.stress
16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.nmds.axes


mothur > nmds(phylip=16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.dist)
Processing Dimension: 2
1
2
3
4
5
6
7
8
9
10

Number of dimensions:   2
Lowest stress :   0
R-squared for configuration:   0

Output File Names: 
16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.nmds.iters
16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.nmds.stress
16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.nmds.axes


mothur > nmds(phylip=16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.dist, mindim=3, maxdim=3)
Processing Dimension: 3
1
2
3
4
5
6
7
8
9
10

Number of dimensions:   3
Lowest stress :   0
R-squared for configuration:   0

Output File Names: 
16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.nmds.iters
16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.nmds.stress
16S.an.unique_list.0.03.rep.phylip.tre1.weighted.phylip.nmds.axes


mothur > amova(phylip=16S.an.unique_list.0.03.rep.phylip.tre1.unweighted.phylip.dist, design=16S.design)
[ERROR]: S01-H0_ATCACG_L001_ is not in your design file, please correct.
[ERROR]: S01-H24_GTAAGT_L001_ is not in your design file, please correct.

mothur > system(echo ok > mothur4.ok )

mothur > quit()

 -- step 6 completed.